What file formats are supported by the VCF Toolkit?

The toolkit supports both VCF (Variant Call Format) and BCF (Binary Call Format) files, including compressed (.vcf.gz) files indexed with tabix.

How do I export variants for a specific gene?

You can use the --region flag followed by the genomic coordinates of the gene to extract and export those specific variants as a structured JSON file or a new VCF.

Do I need external tools like bcftools to use this?

While the toolkit provides its own filtering and stats scripts, it is designed to complement tools like bcftools; you can use the toolkit for inspection and JSON export after initial high-performance pre-filtering.

Can I use this for very large sequencing datasets?

Yes, the toolkit includes a dedicated filtering tool to create subset VCFs and supports region-specific extraction (e.g., --region chr1:1000-2000) to maintain high performance.

VCF Variant Analysis Toolkit

Name: VCF Variant Analysis Toolkit
Author: dakesan

bydakesan

Data Science & ML

Analyzes, filters, and exports genomic variant data from VCF and BCF files for bioinformatics and sequencing workflows.

About

The VCF Toolkit is a specialized suite of scripts designed to streamline the inspection and processing of genomic variants from Whole Genome (WGS) or Whole Exome Sequencing (WES). It enables users to calculate comprehensive variant statistics, apply precision filters based on quality or depth, and export specific genomic regions as JSON for seamless integration into downstream data analysis pipelines. Designed for bioinformatics researchers and developers, this skill provides the necessary tools to handle complex genomic file formats efficiently within the Claude Code environment.

Key Features

Genomic region-specific extraction for targeted analysis of chromosomes or custom coordinates
Built-in error handling and safeguards for large-scale genomic data processing
Flexible variant filtering based on quality (QUAL), depth (DP), and allele frequency (AF)
0 GitHub stars
Comprehensive VCF/BCF statistics including variant counts, quality distributions, and depth stats
JSON export functionality for easy integration with modern data visualization and web tools

Use Cases

Exporting filtered variant sets to JSON format for custom downstream analysis or visualization
Conducting quality control and generating summary reports for WGS/WES sequencing results
Filtering and identifying rare genomic variants for clinical or research discovery

About

Key Features

Genomic region-specific extraction for targeted analysis of chromosomes or custom coordinates
Built-in error handling and safeguards for large-scale genomic data processing
Flexible variant filtering based on quality (QUAL), depth (DP), and allele frequency (AF)
0 GitHub stars
Comprehensive VCF/BCF statistics including variant counts, quality distributions, and depth stats
JSON export functionality for easy integration with modern data visualization and web tools

Use Cases

Exporting filtered variant sets to JSON format for custom downstream analysis or visualization
Conducting quality control and generating summary reports for WGS/WES sequencing results
Filtering and identifying rare genomic variants for clinical or research discovery